Evolution of germline and somatic genomes in the ciliate Chilodonella uncinata The proposed work aims to elucidate principles of molecular evolution that drive the differentiation between the germline (micronuclear) and somatic (macronuclear) genomes of the ciliate Chilodonella uncinata. Ciliates, like most animals, have clearly differentiated germline and somatic genomes;however, in ciliates, these two genomes are housed within each individual cell/organism in contrast to being in separate tissues as in animals. Chilodonella uncinata is a member of the ciliate class Phyllopharyngea and hence has an extensively processed macronuclear genome with millions of gene-sized chromosomes. This property makes it possible to readily separate and analyze loci from both the germline and somatic nuclei of this ciliate species. The proposed work will test three interrelated hypotheses on the nature of gene family evolution between the germline and somatic genomes, the relationship between chromosome amplification and gene expression, and the architecture of heteromeric macronuclei of C. uncinata. Hypotheses will be tested using a combination of molecular approaches (e.g. traditional PCR, walking PCR, high-throughput sequencing of transcriptome) and microscopy tools (e.g. fluorescence in situ hybridization (FISH)). The resulting molecular data will be analyzed using population genetics (e.g. maximum likelihood approaches) and phylogenetic methods, and will be interpreted in light of microscopy images. The outcomes of the proposed work will include furthering knowledge of the biology of C. uncinata and enabling comparisons with other well-studied ciliates (i.e. Tetrahymena and Paramecium). Beyond this specific outcome, combining the results of the proposed work with knowledge of other eukaryotes will provide additional insights into the dynamics of genome evolution across the eukaryotic tree of life. 1) PUBLIC HEALTH RELEVANCE: Microbial organisms provide model systems to explore genome processes and historically have provided insights that are relevant to human health (e.g. discovery of telomeres in ciliates). The proposed work, which focuses on the differences between germline and somatic genomes in a ciliate, has parallels with analyses of changes in somatic genomes associated with aging and disease (i.e. some cancers) in human cells. Hence, the molecular mechanisms elucidated in this study are likely to yield insights into processes analogous to genome changes that impact human health. )